Blank plot for plotLDA()

[xkcococo]

Thanks for providing this package.
I am trying to use it for plotting LDA.

The res table that I get from the function successfully, but when I use:

res <- ldamarker(ps_1,group="breastfeeding_group")
head(res,10)
# A tibble: 10 x 13
# Groups:   rank, tax [10]
   rank  tax      statistic p.value parameter method   p.adj `exclusive brea… `non-exclusive …   max
   <chr> <chr>        <dbl>   <dbl>     <int> <chr>    <dbl>            <dbl>            <dbl> <dbl>
 1 Class D_0__Ar…    1.00   0.316           1 Kruskal… 0.739              NA               NA    NA 
 2 Class D_0__Ba…    0.184  0.668           1 Kruskal… 0.872              NA               NA    NA 
 3 Class D_0__Ba…    1.13   0.288           1 Kruskal… 0.739              NA               NA    NA 
 4 Class D_0__Ba…    1.31   0.253           1 Kruskal… 0.739              NA               NA    NA 
 5 Class D_0__Ba…    0.0412 0.839           1 Kruskal… 0.955              NA               NA    NA 
 6 Class D_0__Ba…    2.28   0.131           1 Kruskal… 0.626              NA               NA    NA 
 7 Class D_0__Ba…    7.41   0.00649         1 Kruskal… 0.287             406.            1861. 1861.
 8 Class D_0__Ba…    3.83   0.0504          1 Kruskal… 0.510              NA               NA    NA 
 9 Class D_0__Ba…    0.169  0.681           1 Kruskal… 0.872              NA               NA    NA 
10 Class D_0__Ba…    0.144  0.704           1 Kruskal… 0.876              NA               NA    NA 
# … with 3 more variables: min <dbl>, LDAscore <dbl>, direction <chr>
plotLDA(res,group=c("exclusive breastfeeding","non-exclusive breastfeeding"),lda=5,pvalue=0.05)

The plot that generated is blank, only has a x-axis label.

Could you help me to address it ?
Thanks!

[guokai8]

Hi @xkcococo,
Could you please check the LDAscore from your results? I am not sure if there are any significant ones meet the cutoff.
Thanks!
Kai

[xkcococo]

@guokai8
Thanks for replying.

I checked the res table and found there are some values in LDAscore table.

Here are all the values that we have in this column except for NA.

> sort(res$LDAscore)
 [1] 2.20 2.20 2.35 2.35 2.35 2.35 2.35 2.43 2.58 2.63 2.63 2.63 2.64 2.69 2.69 2.72 2.80 2.80 2.85
[20] 2.86 2.86 2.86 2.86 2.86 2.86 2.86 2.98 3.04 3.08 3.10 3.16 3.26 3.26 3.29 3.31 3.31 3.31 3.37
[39] 3.42 3.42 3.42 3.42 3.45 3.50 3.53 3.54 3.56 3.56 3.56 3.56 3.56 3.58 3.59 3.60 3.61 3.61 3.61
[58] 3.64 3.72 3.72 3.73 3.73 3.75 3.75 3.78 3.81 3.92 3.92 3.92 3.98 4.07 4.17 4.27 4.30 4.30 4.31
[77] 4.31 4.31 4.49 4.49 4.66 4.84

[guokai8]

Hi @xkcococo,
It seems none of them larger than the cutoff you used (lda=5). Typically, we used lda=2 as the cutoff value.
Kai

[xkcococo]

@guokai8
Thanks for helping!
I was wondering that why we choose lda = 5 as a default setting here? How to interpret that OTU with lda=5? thanks!

[guokai8]

Hi @xkcococo,
The default lda value is 2. And I used the lda value as 5 in the tutorial just because I will have lots of significant ASVs if I used lower value.
Kai

[guokai8]

Set the sig.only=FALSE. Kai

…

On Apr 12, 2021, at 3:17 PM, xkcococo ***@***.***> wrote: @guokai8 <https://github.com/guokai8> I have another question that needs you to help with! Thanks in advance. When I performed plot alpha, I used show,number=TRUE, and pvalue=0.05 as default. But some of the p.values that even larger than 0.05 (not significant shown in the figure), but some did not show. I want all p.values show in figures. Could you help me to address this? Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFKZGZ3EZFZPA7M6XIGHVDTININBANCNFSM42VV2URQ>.

[xkcococo]

@guokai8
Thanks!
When I learned your tutorial, it's really helpful! I really want to apply it to my research!
I noticed there are otu_id in the () of all figures of differential expression and biomarker selection. Is there any way or parameters that only let the y-axis shows the out name instead of with otu id?

Thank you very much!

[guokai8]

Hi @xkcococo,
I am so glad you like it. I used the otu id there just because it is easy to distinguish the bacteria when they had same genus name. And please give me a star if you like the package.
Kai

[xkcococo]

@guokai8 absolutely! Have already given star to this pacakge!
I will keep updating if I have further questions! Thanks a lot!

[guokai8]

@xkcococo Thanks!

[xkcococo]

@guokai8
Hi, I have a question related to log2FC and biomarkers.
Why the results of significant genus (Log2fC) are different from biomarkers (LDA plot)? How to interpret them and the difference between these two results? I think they both mean the difference between the two groups.

[guokai8]

HI @xkcococo,
I think the difference first come from the different methods, but we should have lots of overlap here. Typically I will focus on the shared genus from different methods.
Kai

[xkcococo]

@guokai8
Thanks! I agree!
So all OTUs in lEfSe analysis plot are genus? Or they are OTUs at each level?
Because I confused that some of the OTUs named with multiple '_' of the names and some are not.

[guokai8]

@xkcococo
You can check the results from the ldamarker which show the significant ones at each level.
Kai

[xkcococo]

@guokai8
Hi Kai, I was wondering if it is possible to modify the number of permutations of plotbeta? And what's the default for permutations?

Thanks!